Protective effect of CACNA1A deficiency in oligogenic refractory epilepsy with CACNA1A-CELSR2 digenic mutations.

Objective: The vast majority of refractory epilepsy cases have a complex oligogenic/polygenic origin, which presents a challenge to precision medicine in individual patients. Nonetheless, the high workload and lack of effective guidelines have limited the number of in-depth animal studies.

Methods: Whole-exon sequencing identified a case with refractory epilepsy caused by a combination of two rare and de novo heterozygous variants in CACNA1A and CELSR2, respectively. Polygenic mutation flies were established and logistic regression were applied to study the gene-gene interaction and quantify the seizure-risk weight of epilepsy-associated genes in a polygenic background. In addition, calcium imaging, pharmacology, and transgenic rescue experiments were used to explore the mechanism and the precision medicine strategy for this model.

Results: Seizure-like activity was mitigated in the Cacna1a-Celsr2 digenic knockdown flies, whereas it was aggravated in the Cacna1a knockin-Celsr2 knockdown flies, and all relevant monogenic mutation flies showed seizures. Logistic regression suggested that the Cacna1a deficiency provided a protective effect against seizures in Celsr2 knockdown flies. The severe seizures from Cacna1a knockin-Celsr2 knockdown, the genotype mimicking that of the patient, can be completely rescued by inhibiting the calcium channel via genetic (Cacna1a knockdown) or pharmacologic (pregabalin) treatment during a limited period of development. Calcium imaging results suggested a synaptic cleft balance mechanism for the protective effect of CACNA1A deficiency in the polygenic background.

Significance: CACNA1A presented multiple effects on epileptogenesis in diverse genetic backgrounds and provided an effective preclinical approach to clarify the net impact of polygenic variants for designing a precisive medicine strategy against refractory epilepsy.